Research workbench
Catalytically inactive yeast pseudouridine synthase, PUS1, bound to RNA
Analyse Catalytically inactive yeast pseudouridine synthase, PUS1, bound to RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R9G
- Type
- protein + RNA
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA pseudouridine synthase 1; RNA (5'- R(*AP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP…
- EC
- 5.4.99.-
- UniProt
- Q12211
- Ligands
- SO4, CL
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA pseudouridine synthase 1 (EC 5.4.99.-) | protein | 386 | 39% helix, 19% strand | Q12211 |
| B | RNA (5'- R(*AP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3') | rna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.60 | 0.84 | 24 | SO4, CL |
| 2 | 338 | 0.59 | 0.77 | 40 | empty |
| 3 | 107 | 0.54 | 0.83 | 24 | empty |
| 4 | 88 | 0.44 | 0.79 | 18 | empty |
| 5 | 79 | 0.38 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 475 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7R9G · Catalytically inactive yeast Pseudouridine Synthase, PUS1, bound to RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q12211 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase 1 (Q12211) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q12211
- Elsewhere: RCSB PDB 7R9G · PDBe 7R9G · UniProt Q12211
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